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Pair tumor and normal BAMs regardless of per-BAM kinetics - #219
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robert-a-forsyth wants to merge 3 commits into
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Tumor/normal pairing joined on a meta that carried METAEXTRACT's per-BAM `kinetics` flag, so a pair where only one BAM kept PacBio kinetics was silently dropped from all variant calling; its QC still reached the report join, which then crashed with "Invalid method invocation call". - Drop `kinetics` from meta after alignment; only the m6A branch reads it. - Stop early when a sample's BAMs resolve to different Clair models (validateSampleModels), since those also key the pairing joins. - Make the tumor/normal join failOnMismatch so meta drift can no longer drop a pair silently. Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
![claude[bot]](https://avatars.githubusercontent.com/in/1236702?s=60&v=4){kind=small}
| } | ||
| .join(paired_normal_bams) | ||
| // failOnMismatch: a tumor/normal meta drift must stop the run, not drop the pair | ||
| .join(paired_normal_bams, failOnMismatch: true) |
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No regression test for the bug this PR fixes. The only new tests are the two validateSampleModels function tests. They don't run the pairing join itself.
Nothing tagged small covers a paired PacBio sample where one BAM has kinetics and the other doesn't, so CI never runs that case. The core fix (dropping kinetics from the subMaps) and the new failOnMismatch: true are therefore only checked indirectly.
Suggestions:
- Add a
smallstub or fixture test with a tumor/normal pair whose METAEXTRACTkineticsdiffers. It should show thatsomatic_smallvar_inputemits the pair and that the run reachesLRSOMATICREPORT. - If that isn't practical, run the Slurm test array with such a samplesheet and note the result in the PR.
| ch_samplesheet | ||
| .map { meta, _bam -> meta } | ||
| .collect() | ||
| .map { metas -> validateSampleModels(metas) } |
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Missing CHANGELOG.md entry. The PR changes behaviour that users will see:
- Paired samples whose BAMs differ in kinetics are no longer dropped silently.
- A run with mismatched per-BAM caller models now stops with an error.
- The tumor/normal join now uses
failOnMismatch.
REVIEW.md asks for an entry under v1.2.0dev that cites #219. This should probably go under Fixed, and possibly Changed for the new launch-time error.
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Automated review: 2 findings, posted inline.
The fix itself looks right. I removed A human reviewer needs to run these, because I couldn't run anything:
🤖 Generated with Claude Code |
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Co-Authored-By: Claude Opus 5.5 (1M context) <noreply@anthropic.com>
#223 combined the Severus, Wakhan and SAVANA inputs into one shared sv_meta_keys list built from PHASING_HAPLOTYPING's haplotagged BAMs, and it carried 'kinetics'. Take dev's structure and drop 'kinetics' from that list too, so it matches the kinetics-free phased germline VCF meta it joins with. Co-Authored-By: Claude Opus 5.5 <noreply@anthropic.com>
Collaborator
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Merged current Conflict in def sv_meta_keys = ['id', 'paired_data', 'platform', 'sex', 'fiber',
'clair3_model', 'clairS_model', 'clairSTO_model']Checks that nothing needs it there:
Lint: nf-test (apptainer, Slurm array 11767781, merge commit bf6bf58). Every pipeline snapshot matched with no re-recording:
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Tumor/normal pairing joined on a meta that carried METAEXTRACT's per-BAM
kineticsflag, so a pair where only one BAM kept PacBio kinetics was silently dropped from all variant calling; its QC still reached the report join, which then crashed with "Invalid method invocation call".kineticsfrom meta after alignment; only the m6A branch reads it.PR checklist
nf-core pipelines lint).nextflow run . -profile test,docker --outdir <OUTDIR>).nextflow run . -profile debug,test,docker --outdir <OUTDIR>).docs/usage.mdis updated.docs/output.mdis updated.CHANGELOG.mdis updated.README.mdis updated (including new tool citations and authors/contributors).